Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy-Reference-Cited by-同舟云学术

Comparison of Different HIV-1 Resistance Interpretation Tools for Next-Generation Sequencing in Italy

Published:2024-09-06 Issue:9 Volume:16 Page:1422
ISSN:1999-4915
Container-title:Viruses
language:en
Short-container-title:Viruses

Author:

Armenia Daniele¹,Carioti Luca²^ORCID,Micheli Valeria³^ORCID,Bon Isabella⁴,Allice Tiziano⁵,Bonura Celestino⁶,Bruzzone Bianca⁷,Bracchitta Fiorenza³,Cerutti Francesco⁵^ORCID,Giammanco Giovanni Maurizio⁶^ORCID,Stefanelli Federica⁷,Bonifacio Maria Addolorata⁸^ORCID,Bertoli Ada⁹,Vatteroni Marialinda¹⁰,Ibba Gabriele¹¹,Novazzi Federica¹²^ORCID,Lipsi Maria Rosaria¹³,Cuomo Nunzia¹⁴,Vicenti Ilaria¹⁵^ORCID,Ceccherini-Silberstein Francesca²,Rossetti Barbara¹⁶^ORCID,Bezenchek Antonia¹⁷¹⁸^ORCID,Saladini Francesco¹⁵^ORCID,Zazzi Maurizio¹⁵^ORCID,Santoro Maria Mercedes²^ORCID

Affiliation:

1. Departmental Faculty, UniCamillus, Saint Camillus International University of Health Sciences, 00131 Rome, Italy

2. Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy

3. Laboratory of Clinical Microbiology, Virology and Bioemergencies, ASST Fatebenefratelli Sacco-University of Milan, 20157 Milan, Italy

4. Microbiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy

5. Laboratory of Microbiology and Virology, Amedeo di Savoia Hospital, 10149 Turin, Italy

6. Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza “G. D’Alessandro” (PROSAMI), Azienda Ospedaliera Universitaria Policlinico “P. Giaccone”-University of Palermo, 90127 Palermo, Italy

7. Hygiene Unit, Ospedale Policlinico San Martino, 16132 Genoa, Italy

8. Section of Experimental and Clinical Pathology, Department of Precision and Regenerative Medicine and Jonic Area, University of Bari, 70121 Bari, Italy

9. Virology Unit, Polyclinic of “Tor Vergata”, 00133 Rome, Italy

10. Virology Unit, AOU Pisana, 56126 Pisa, Italy

11. Microbiology and Virology Unit, Diagnostic Department, AOU Sassari, 07100 Sassari, Italy

12. Department of Medicine and Technological Innovation, University of Insubria, 21100 Varese, Italy

13. Microbiology and Virology Unit, Policlinico Riuniti Foggia Hospital, 71121 Foggia, Italy

14. U.O.C. Microbiologia e Virologia, P.O. “D.Cotugno”-AO dei Colli, 80100 Napoli, Italy

15. Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy

16. Infectious Disease Department, USL SUDEST, Toscana, Misericordia Hospital, 58100 Grosseto, Italy

17. IPRO-InformaPRO S.r.l., 00152 Rome, Italy

18. EuResist Network GEIE, 00152 Rome, Italy

Abstract

Background: Next-generation sequencing (NGS) is gradually replacing Sanger sequencing for HIV genotypic drug resistance testing (GRT). This work evaluated the concordance among different NGS-GRT interpretation tools in a real-life setting. Methods: Routine NGS-GRT data were generated from viral RNA at 11 Italian laboratories with the AD4SEQ HIV-1 Solution v2 commercial kit. NGS results were interpreted by the SmartVir system provided by the kit and by two online tools (HyDRA Web and Stanford HIVdb). NGS-GRT was considered valid when the coverage was >100 reads (100×) at each PR/RT/IN resistance-associated position listed in the HIVdb 9.5.1 algorithm. Results: Among 629 NGS-GRT, 75.2%, 74.2%, and 70.9% were valid according to SmartVir, HyDRA Web, and HIVdb. Considering at least two interpretation tools, 463 (73.6%) NGS-GRT had a valid coverage for resistance analyses. The proportion of valid samples was affected by viremia <10,000–1000 copies/mL and non-B subtypes. Mutations at an NGS frequency >10% showed fair concordance among different interpretation tools. Conclusion: This Italian survey on NGS resistance testing suggests that viremia levels and HIV subtype affect NGS-GRT coverage. Within the current routine method for NGS-GRT, only mutations with frequency >10% seem reliably detected across different interpretation tools.

Publisher

MDPI AG

Link

https://www.mdpi.com/1999-4915/16/9/1422/pdf

Reference30 articles.

1. European AIDS Clinical Society (2024, July 31). Guidelines—Version 12.0. Available online: https://www.eacsociety.org/media/guidelines-12.0.pdf.

2. (2024, July 31). Panel on Antiretroviral Guidelines for Adults and Adolescents, Guidelines for the Use of Antiretroviral Agents in Adults and Adolescents with HIV, Department of Health and Human Services, Available online: https://clinicalinfo.hiv.gov/sites/default/files/guidelines/documents/adult-adolescent-arv/guidelines-adult-adolescent-arv.pdf.

3. Parkin, N.T., Avila-Rios, S., Bibby, D.F., Brumme, C.J., Eshleman, S.H., Harrigan, P.R., Howison, M., Hunt, G., Ji, H., and Kantor, R. (2020). Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping. Viruses, 12.

4. Shall I Trust the Report? Variable Performance of Sanger Sequencing Revealed by Deep Sequencing on HIV Drug Resistance Mutation Detection;Chen;Int. J. Infect. Dis.,2020

5. PRESTIGIO RING: “A 59-year-old HIV-1 positive, highly treatment-experienced woman failing darunavir/ritonavir plus raltegravir”;Labate;New Microbiol.,2023